I have two questions.
How to for loop .fastq files which are in a single directory in cutadapt?
for file in *.fastq; do cutadapt -a AACTGTCGGCACCATCTA -o cell_line_output.fastq cell_line.fastq
This one gives me an error.
And, also, how to change output files names for every loop, for example, cell_line_1_output.fastq, cell_line_2_output.fastq?